Genes & Genomics

, Volume 37, Issue 1, pp 87–95 | Cite as

TE composition of human long noncoding RNAs and their expression patterns in human tissues

  • Donghee Kang
  • Yun-Ji Kim
  • Kwonho Hong
  • Kyudong Han
Research Article

Abstract

High-throughput sequencing analyses have revealed that transposable elements (TEs) comprise approximately half of the human genome and frequently involved in genomic rearrangements and instability by various mechanisms. Interestingly, many noncoding RNAs (ncRNAs) contain TEs and the TE-containing ncRNAs that have been implicated in cellular processes and various diseases in mammals. In this study, we retrieved 94 human long noncoding RNAs (lncRNAs; >200 nucleotides in length) from lncRNAdb and analyzed TEs which are embedded within the lncRNAs, focusing on their chromosomal distribution. The result showed that TEs occupy ~27 % of the lncRNA transcripts in mass and lncRNA containing TEs are enriched in human chromosome 11. We further analyzed subfamily of the TEs and found that most of the TEs belong to AluSx and L1 which are the most successful TE subfamilies in the human genome. Numerous lncRNAs have been reported to be expressed in a cell-type specific manner. Thus, using reverse transcription PCR with specific primers for the lncRNAs, we examined their expression pattern in human normal tissues and cancer cells. Most of the lncRNAs were universally amplified from 20 different types of normal human tissues but some of them displayed tissue-specific expression. Especially, 11 lncRNAs were expressed only in human cancer cells, implying the possibility of their involvement in carcinogenesis.

Keywords

Expression pattern Gene composition Human genome Long noncoding RNAs Transposable elements 

Supplementary material

13258_2014_232_MOESM1_ESM.pdf (77 kb)
Supplementary material 1 (PDF 77 kb)
13258_2014_232_MOESM2_ESM.pdf (33 kb)
Supplementary material 2 (PDF 32 kb)

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Copyright information

© The Genetics Society of Korea and Springer-Science and Media 2014

Authors and Affiliations

  • Donghee Kang
    • 1
  • Yun-Ji Kim
    • 1
    • 2
  • Kwonho Hong
    • 1
  • Kyudong Han
    • 1
    • 2
  1. 1.Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative MedicineDankook UniversityCheonanRepublic of Korea
  2. 2.DKU-Theragen Institute for NGS Analysis (DTiNa)CheonanRepublic of Korea

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